Multiple sequence alignment - TraesCS1A01G083700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G083700 chr1A 100.000 2437 0 0 1 2437 68302858 68300422 0 4501
1 TraesCS1A01G083700 chr2D 94.226 1351 74 4 1 1349 476878769 476880117 0 2060
2 TraesCS1A01G083700 chr2D 93.939 1353 75 7 1 1349 349010866 349009517 0 2037
3 TraesCS1A01G083700 chr2D 94.599 685 35 2 1754 2437 65570040 65570723 0 1059
4 TraesCS1A01G083700 chr2D 95.227 419 17 2 1346 1761 370188190 370187772 0 660
5 TraesCS1A01G083700 chr1D 94.358 1347 69 7 7 1349 495409685 495408342 0 2060
6 TraesCS1A01G083700 chr1D 94.100 1356 71 7 1 1349 110658784 110657431 0 2052
7 TraesCS1A01G083700 chr1D 94.013 1353 73 6 1 1349 470557430 470556082 0 2043
8 TraesCS1A01G083700 chr1D 94.013 1353 74 7 1 1349 471280900 471282249 0 2043
9 TraesCS1A01G083700 chr1D 94.469 687 34 4 1754 2437 414581316 414582001 0 1055
10 TraesCS1A01G083700 chr1D 95.673 416 18 0 1346 1761 61780979 61780564 0 669
11 TraesCS1A01G083700 chr6D 94.022 1355 73 7 1 1349 31859059 31860411 0 2047
12 TraesCS1A01G083700 chr3D 93.953 1356 67 9 1 1349 578843871 578845218 0 2036
13 TraesCS1A01G083700 chr5D 93.865 1353 75 8 1 1349 12933483 12932135 0 2032
14 TraesCS1A01G083700 chr7D 94.752 686 33 3 1754 2437 629877942 629878626 0 1064
15 TraesCS1A01G083700 chr7D 94.599 685 35 2 1754 2437 123446729 123446046 0 1059
16 TraesCS1A01G083700 chr7D 94.599 685 36 1 1754 2437 460630029 460629345 0 1059
17 TraesCS1A01G083700 chr7D 94.606 686 34 3 1754 2437 544981464 544980780 0 1059
18 TraesCS1A01G083700 chr7D 94.461 686 33 4 1754 2437 229348334 229349016 0 1051
19 TraesCS1A01G083700 chr7D 95.923 417 15 1 1346 1760 37281273 37281689 0 675
20 TraesCS1A01G083700 chr7D 94.737 418 21 1 1346 1762 75161429 75161846 0 649
21 TraesCS1A01G083700 chr7D 94.724 417 21 1 1346 1761 602283083 602283499 0 647
22 TraesCS1A01G083700 chr7A 94.453 685 36 2 1754 2437 48154756 48155439 0 1053
23 TraesCS1A01G083700 chr7A 95.215 418 18 1 1346 1761 168463595 168464012 0 660
24 TraesCS1A01G083700 chr3A 94.461 686 35 3 1754 2437 362693668 362692984 0 1053
25 TraesCS1A01G083700 chr3A 95.146 412 19 1 1347 1758 479180045 479180455 0 649
26 TraesCS1A01G083700 chr6A 95.433 416 19 0 1346 1761 107047435 107047020 0 664
27 TraesCS1A01G083700 chr5A 94.952 416 17 4 1346 1760 544022783 544023195 0 649


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G083700 chr1A 68300422 68302858 2436 True 4501 4501 100.000 1 2437 1 chr1A.!!$R1 2436
1 TraesCS1A01G083700 chr2D 476878769 476880117 1348 False 2060 2060 94.226 1 1349 1 chr2D.!!$F2 1348
2 TraesCS1A01G083700 chr2D 349009517 349010866 1349 True 2037 2037 93.939 1 1349 1 chr2D.!!$R1 1348
3 TraesCS1A01G083700 chr2D 65570040 65570723 683 False 1059 1059 94.599 1754 2437 1 chr2D.!!$F1 683
4 TraesCS1A01G083700 chr1D 495408342 495409685 1343 True 2060 2060 94.358 7 1349 1 chr1D.!!$R4 1342
5 TraesCS1A01G083700 chr1D 110657431 110658784 1353 True 2052 2052 94.100 1 1349 1 chr1D.!!$R2 1348
6 TraesCS1A01G083700 chr1D 470556082 470557430 1348 True 2043 2043 94.013 1 1349 1 chr1D.!!$R3 1348
7 TraesCS1A01G083700 chr1D 471280900 471282249 1349 False 2043 2043 94.013 1 1349 1 chr1D.!!$F2 1348
8 TraesCS1A01G083700 chr1D 414581316 414582001 685 False 1055 1055 94.469 1754 2437 1 chr1D.!!$F1 683
9 TraesCS1A01G083700 chr6D 31859059 31860411 1352 False 2047 2047 94.022 1 1349 1 chr6D.!!$F1 1348
10 TraesCS1A01G083700 chr3D 578843871 578845218 1347 False 2036 2036 93.953 1 1349 1 chr3D.!!$F1 1348
11 TraesCS1A01G083700 chr5D 12932135 12933483 1348 True 2032 2032 93.865 1 1349 1 chr5D.!!$R1 1348
12 TraesCS1A01G083700 chr7D 629877942 629878626 684 False 1064 1064 94.752 1754 2437 1 chr7D.!!$F5 683
13 TraesCS1A01G083700 chr7D 123446046 123446729 683 True 1059 1059 94.599 1754 2437 1 chr7D.!!$R1 683
14 TraesCS1A01G083700 chr7D 460629345 460630029 684 True 1059 1059 94.599 1754 2437 1 chr7D.!!$R2 683
15 TraesCS1A01G083700 chr7D 544980780 544981464 684 True 1059 1059 94.606 1754 2437 1 chr7D.!!$R3 683
16 TraesCS1A01G083700 chr7D 229348334 229349016 682 False 1051 1051 94.461 1754 2437 1 chr7D.!!$F3 683
17 TraesCS1A01G083700 chr7A 48154756 48155439 683 False 1053 1053 94.453 1754 2437 1 chr7A.!!$F1 683
18 TraesCS1A01G083700 chr3A 362692984 362693668 684 True 1053 1053 94.461 1754 2437 1 chr3A.!!$R1 683

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
313 317 0.731514 CGAACGCCTTCGCTACTTCA 60.732 55.0 4.93 0.0 42.72 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1702 0.178944 TTTCGTCTCTCCTCCCACCA 60.179 55.0 0.0 0.0 0.0 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 204 2.184322 GCTTGCTCGATCCCGTCA 59.816 61.111 0.00 0.00 37.05 4.35
208 212 1.000827 CTCGATCCCGTCAATCTGGAG 60.001 57.143 0.00 0.00 33.15 3.86
269 273 4.453892 GCCATTGCCCTCCCTGCT 62.454 66.667 0.00 0.00 0.00 4.24
285 289 1.194121 TGCTGGCTAGGAGCTTGTCA 61.194 55.000 0.00 0.00 41.99 3.58
313 317 0.731514 CGAACGCCTTCGCTACTTCA 60.732 55.000 4.93 0.00 42.72 3.02
361 365 4.829518 CCGCATCGACGTCGCTGA 62.830 66.667 37.30 21.36 37.65 4.26
395 399 3.302344 GGGCCACCGCAACATTGT 61.302 61.111 4.39 0.00 36.38 2.71
435 439 3.346734 GCCCCCATGTCTTCCCCA 61.347 66.667 0.00 0.00 0.00 4.96
513 523 5.232463 TCGTTTGCTCTCGTTAGGTATTTT 58.768 37.500 0.00 0.00 0.00 1.82
528 538 0.965363 ATTTTGCCGTGGCCGAGAAT 60.965 50.000 8.69 0.85 41.09 2.40
533 543 2.264480 CGTGGCCGAGAATCACCA 59.736 61.111 0.00 0.00 38.52 4.17
552 562 3.542676 CCGCCATGGCCATTGCAT 61.543 61.111 33.77 6.27 40.13 3.96
594 604 2.424842 ATTGACCCCGTGGCACATGT 62.425 55.000 19.09 10.82 45.33 3.21
639 650 2.665000 CCTGCCGCTCTTCTTCCA 59.335 61.111 0.00 0.00 0.00 3.53
691 702 4.710695 CCGTGCTACACCGCGTCA 62.711 66.667 4.92 0.00 37.03 4.35
756 769 2.983030 GTGCCCCATGCGACACAA 60.983 61.111 5.61 0.00 45.60 3.33
897 912 3.105928 GCCCACCCCCTCATCCAT 61.106 66.667 0.00 0.00 0.00 3.41
958 973 3.048475 CTGCTGCGTGCTGCTTCT 61.048 61.111 21.57 0.00 46.63 2.85
961 976 2.901292 GCTGCGTGCTGCTTCTTGT 61.901 57.895 15.32 0.00 46.63 3.16
1100 1115 3.933542 GAGGCAGGAGGTCTGGGGT 62.934 68.421 0.00 0.00 43.54 4.95
1208 1226 5.832539 AAATCATAACCCGGAGATCTCAT 57.167 39.130 23.85 5.16 0.00 2.90
1210 1228 4.873746 TCATAACCCGGAGATCTCATTC 57.126 45.455 23.85 6.25 0.00 2.67
1356 1376 2.132740 CAAATGGGGTTTGTGACGTG 57.867 50.000 0.00 0.00 41.80 4.49
1357 1377 1.407258 CAAATGGGGTTTGTGACGTGT 59.593 47.619 0.00 0.00 41.80 4.49
1358 1378 1.314730 AATGGGGTTTGTGACGTGTC 58.685 50.000 0.00 0.00 0.00 3.67
1359 1379 0.472471 ATGGGGTTTGTGACGTGTCT 59.528 50.000 0.00 0.00 0.00 3.41
1360 1380 0.462937 TGGGGTTTGTGACGTGTCTG 60.463 55.000 0.00 0.00 0.00 3.51
1361 1381 0.179067 GGGGTTTGTGACGTGTCTGA 60.179 55.000 0.00 0.00 0.00 3.27
1362 1382 1.542547 GGGGTTTGTGACGTGTCTGAT 60.543 52.381 0.00 0.00 0.00 2.90
1363 1383 2.218603 GGGTTTGTGACGTGTCTGATT 58.781 47.619 0.00 0.00 0.00 2.57
1364 1384 3.395639 GGGTTTGTGACGTGTCTGATTA 58.604 45.455 0.00 0.00 0.00 1.75
1365 1385 3.432252 GGGTTTGTGACGTGTCTGATTAG 59.568 47.826 0.00 0.00 0.00 1.73
1366 1386 3.432252 GGTTTGTGACGTGTCTGATTAGG 59.568 47.826 0.00 0.00 0.00 2.69
1367 1387 4.304110 GTTTGTGACGTGTCTGATTAGGA 58.696 43.478 0.00 0.00 0.00 2.94
1368 1388 4.594123 TTGTGACGTGTCTGATTAGGAA 57.406 40.909 0.00 0.00 0.00 3.36
1369 1389 4.594123 TGTGACGTGTCTGATTAGGAAA 57.406 40.909 0.00 0.00 0.00 3.13
1370 1390 4.556233 TGTGACGTGTCTGATTAGGAAAG 58.444 43.478 0.00 0.00 0.00 2.62
1371 1391 4.038763 TGTGACGTGTCTGATTAGGAAAGT 59.961 41.667 0.00 0.00 0.00 2.66
1372 1392 4.989168 GTGACGTGTCTGATTAGGAAAGTT 59.011 41.667 0.00 0.00 0.00 2.66
1373 1393 5.465724 GTGACGTGTCTGATTAGGAAAGTTT 59.534 40.000 0.00 0.00 0.00 2.66
1374 1394 5.465390 TGACGTGTCTGATTAGGAAAGTTTG 59.535 40.000 0.00 0.00 0.00 2.93
1375 1395 4.213482 ACGTGTCTGATTAGGAAAGTTTGC 59.787 41.667 0.00 0.00 0.00 3.68
1376 1396 4.213270 CGTGTCTGATTAGGAAAGTTTGCA 59.787 41.667 9.95 0.00 0.00 4.08
1377 1397 5.277779 CGTGTCTGATTAGGAAAGTTTGCAA 60.278 40.000 9.95 0.00 0.00 4.08
1378 1398 6.503524 GTGTCTGATTAGGAAAGTTTGCAAA 58.496 36.000 8.05 8.05 0.00 3.68
1379 1399 7.147976 GTGTCTGATTAGGAAAGTTTGCAAAT 58.852 34.615 16.21 0.00 0.00 2.32
1380 1400 7.115378 GTGTCTGATTAGGAAAGTTTGCAAATG 59.885 37.037 16.21 0.00 0.00 2.32
1381 1401 7.147976 GTCTGATTAGGAAAGTTTGCAAATGT 58.852 34.615 16.21 2.99 0.00 2.71
1382 1402 7.653311 GTCTGATTAGGAAAGTTTGCAAATGTT 59.347 33.333 16.21 12.22 0.00 2.71
1383 1403 8.855110 TCTGATTAGGAAAGTTTGCAAATGTTA 58.145 29.630 16.21 0.54 0.00 2.41
1384 1404 9.474920 CTGATTAGGAAAGTTTGCAAATGTTAA 57.525 29.630 16.21 9.01 0.00 2.01
1385 1405 9.474920 TGATTAGGAAAGTTTGCAAATGTTAAG 57.525 29.630 16.21 0.00 0.00 1.85
1386 1406 9.691362 GATTAGGAAAGTTTGCAAATGTTAAGA 57.309 29.630 16.21 0.00 0.00 2.10
1388 1408 9.877178 TTAGGAAAGTTTGCAAATGTTAAGAAA 57.123 25.926 16.21 2.11 0.00 2.52
1389 1409 8.196802 AGGAAAGTTTGCAAATGTTAAGAAAC 57.803 30.769 16.21 0.00 36.07 2.78
1390 1410 8.040727 AGGAAAGTTTGCAAATGTTAAGAAACT 58.959 29.630 16.21 0.90 35.65 2.66
1391 1411 9.308318 GGAAAGTTTGCAAATGTTAAGAAACTA 57.692 29.630 16.21 0.00 33.60 2.24
1409 1429 9.601810 AAGAAACTATTTATTGGGAGGAAAGTT 57.398 29.630 0.00 0.00 0.00 2.66
1410 1430 9.025041 AGAAACTATTTATTGGGAGGAAAGTTG 57.975 33.333 0.00 0.00 0.00 3.16
1411 1431 8.721133 AAACTATTTATTGGGAGGAAAGTTGT 57.279 30.769 0.00 0.00 0.00 3.32
1412 1432 7.703058 ACTATTTATTGGGAGGAAAGTTGTG 57.297 36.000 0.00 0.00 0.00 3.33
1413 1433 7.466804 ACTATTTATTGGGAGGAAAGTTGTGA 58.533 34.615 0.00 0.00 0.00 3.58
1414 1434 6.590234 ATTTATTGGGAGGAAAGTTGTGAC 57.410 37.500 0.00 0.00 0.00 3.67
1415 1435 1.961793 TTGGGAGGAAAGTTGTGACG 58.038 50.000 0.00 0.00 0.00 4.35
1416 1436 0.834612 TGGGAGGAAAGTTGTGACGT 59.165 50.000 0.00 0.00 0.00 4.34
1417 1437 1.226746 GGGAGGAAAGTTGTGACGTG 58.773 55.000 0.00 0.00 0.00 4.49
1418 1438 1.474498 GGGAGGAAAGTTGTGACGTGT 60.474 52.381 0.00 0.00 0.00 4.49
1419 1439 1.865340 GGAGGAAAGTTGTGACGTGTC 59.135 52.381 0.00 0.00 0.00 3.67
1420 1440 2.483188 GGAGGAAAGTTGTGACGTGTCT 60.483 50.000 0.00 0.00 0.00 3.41
1421 1441 2.540101 GAGGAAAGTTGTGACGTGTCTG 59.460 50.000 0.00 0.00 0.00 3.51
1422 1442 2.093658 AGGAAAGTTGTGACGTGTCTGT 60.094 45.455 0.00 0.00 0.00 3.41
1423 1443 2.676342 GGAAAGTTGTGACGTGTCTGTT 59.324 45.455 0.00 0.00 0.00 3.16
1424 1444 3.866910 GGAAAGTTGTGACGTGTCTGTTA 59.133 43.478 0.00 0.00 0.00 2.41
1425 1445 4.510340 GGAAAGTTGTGACGTGTCTGTTAT 59.490 41.667 0.00 0.00 0.00 1.89
1426 1446 5.007332 GGAAAGTTGTGACGTGTCTGTTATT 59.993 40.000 0.00 0.00 0.00 1.40
1427 1447 6.431198 AAAGTTGTGACGTGTCTGTTATTT 57.569 33.333 0.00 0.00 0.00 1.40
1428 1448 5.403897 AGTTGTGACGTGTCTGTTATTTG 57.596 39.130 0.00 0.00 0.00 2.32
1429 1449 4.873827 AGTTGTGACGTGTCTGTTATTTGT 59.126 37.500 0.00 0.00 0.00 2.83
1430 1450 5.353123 AGTTGTGACGTGTCTGTTATTTGTT 59.647 36.000 0.00 0.00 0.00 2.83
1431 1451 5.804692 TGTGACGTGTCTGTTATTTGTTT 57.195 34.783 0.00 0.00 0.00 2.83
1432 1452 5.802064 TGTGACGTGTCTGTTATTTGTTTC 58.198 37.500 0.00 0.00 0.00 2.78
1433 1453 5.202640 GTGACGTGTCTGTTATTTGTTTCC 58.797 41.667 0.00 0.00 0.00 3.13
1434 1454 5.007332 GTGACGTGTCTGTTATTTGTTTCCT 59.993 40.000 0.00 0.00 0.00 3.36
1435 1455 6.201425 GTGACGTGTCTGTTATTTGTTTCCTA 59.799 38.462 0.00 0.00 0.00 2.94
1436 1456 6.762187 TGACGTGTCTGTTATTTGTTTCCTAA 59.238 34.615 0.00 0.00 0.00 2.69
1437 1457 7.280428 TGACGTGTCTGTTATTTGTTTCCTAAA 59.720 33.333 0.00 0.00 0.00 1.85
1438 1458 7.987649 ACGTGTCTGTTATTTGTTTCCTAAAA 58.012 30.769 0.00 0.00 0.00 1.52
1439 1459 7.911727 ACGTGTCTGTTATTTGTTTCCTAAAAC 59.088 33.333 0.00 0.00 44.18 2.43
1532 1552 9.883142 TTTGTTTCCTGAAAATCTGTTATTTGT 57.117 25.926 0.00 0.00 31.33 2.83
1533 1553 9.883142 TTGTTTCCTGAAAATCTGTTATTTGTT 57.117 25.926 0.00 0.00 31.33 2.83
1534 1554 9.883142 TGTTTCCTGAAAATCTGTTATTTGTTT 57.117 25.926 0.00 0.00 31.33 2.83
1536 1556 9.541143 TTTCCTGAAAATCTGTTATTTGTTTCC 57.459 29.630 0.00 0.00 0.00 3.13
1537 1557 8.477419 TCCTGAAAATCTGTTATTTGTTTCCT 57.523 30.769 0.00 0.00 0.00 3.36
1538 1558 9.581289 TCCTGAAAATCTGTTATTTGTTTCCTA 57.419 29.630 0.00 0.00 0.00 2.94
1553 1573 7.411486 TTGTTTCCTAAGACAAATTGAACCA 57.589 32.000 0.00 0.00 33.19 3.67
1554 1574 7.411486 TGTTTCCTAAGACAAATTGAACCAA 57.589 32.000 0.00 0.00 0.00 3.67
1555 1575 8.017418 TGTTTCCTAAGACAAATTGAACCAAT 57.983 30.769 0.00 0.00 35.39 3.16
1556 1576 9.137459 TGTTTCCTAAGACAAATTGAACCAATA 57.863 29.630 0.00 0.00 32.43 1.90
1557 1577 9.974980 GTTTCCTAAGACAAATTGAACCAATAA 57.025 29.630 0.00 0.00 32.43 1.40
1561 1581 9.423061 CCTAAGACAAATTGAACCAATAAAAGG 57.577 33.333 0.00 0.00 32.43 3.11
1565 1585 9.710900 AGACAAATTGAACCAATAAAAGGAATC 57.289 29.630 0.00 0.00 32.43 2.52
1566 1586 8.532977 ACAAATTGAACCAATAAAAGGAATCG 57.467 30.769 0.00 0.00 32.43 3.34
1567 1587 8.364142 ACAAATTGAACCAATAAAAGGAATCGA 58.636 29.630 0.00 0.00 32.43 3.59
1568 1588 9.369904 CAAATTGAACCAATAAAAGGAATCGAT 57.630 29.630 0.00 0.00 32.43 3.59
1569 1589 9.942850 AAATTGAACCAATAAAAGGAATCGATT 57.057 25.926 11.20 11.20 32.43 3.34
1570 1590 8.931385 ATTGAACCAATAAAAGGAATCGATTG 57.069 30.769 16.96 0.00 31.77 2.67
1571 1591 7.695480 TGAACCAATAAAAGGAATCGATTGA 57.305 32.000 16.96 0.00 30.62 2.57
1572 1592 8.292444 TGAACCAATAAAAGGAATCGATTGAT 57.708 30.769 16.96 0.06 35.98 2.57
1574 1594 9.586435 GAACCAATAAAAGGAATCGATTGATTT 57.414 29.630 16.96 14.79 44.79 2.17
1575 1595 8.931385 ACCAATAAAAGGAATCGATTGATTTG 57.069 30.769 16.96 8.94 44.79 2.32
1576 1596 7.492344 ACCAATAAAAGGAATCGATTGATTTGC 59.508 33.333 16.96 0.00 44.79 3.68
1577 1597 7.492020 CCAATAAAAGGAATCGATTGATTTGCA 59.508 33.333 16.96 8.16 44.79 4.08
1578 1598 9.037737 CAATAAAAGGAATCGATTGATTTGCAT 57.962 29.630 16.96 9.83 44.79 3.96
1582 1602 9.603921 AAAAGGAATCGATTGATTTGCATAATT 57.396 25.926 16.96 0.00 44.79 1.40
1583 1603 9.603921 AAAGGAATCGATTGATTTGCATAATTT 57.396 25.926 16.96 2.14 44.79 1.82
1590 1610 9.734620 TCGATTGATTTGCATAATTTAAGGAAG 57.265 29.630 0.00 0.00 0.00 3.46
1591 1611 9.520204 CGATTGATTTGCATAATTTAAGGAAGT 57.480 29.630 0.00 0.00 0.00 3.01
1619 1639 9.225682 AGATCCTTGATTTGTTATAGGTTAGGA 57.774 33.333 0.00 0.00 33.07 2.94
1620 1640 9.847224 GATCCTTGATTTGTTATAGGTTAGGAA 57.153 33.333 0.00 0.00 32.36 3.36
1622 1642 9.681062 TCCTTGATTTGTTATAGGTTAGGAAAG 57.319 33.333 0.00 0.00 0.00 2.62
1623 1643 9.462606 CCTTGATTTGTTATAGGTTAGGAAAGT 57.537 33.333 0.00 0.00 0.00 2.66
1637 1657 8.877195 AGGTTAGGAAAGTTCTAGTTGTAATGA 58.123 33.333 0.00 0.00 0.00 2.57
1638 1658 9.498176 GGTTAGGAAAGTTCTAGTTGTAATGAA 57.502 33.333 0.00 0.00 0.00 2.57
1642 1662 8.652290 AGGAAAGTTCTAGTTGTAATGAAGAGT 58.348 33.333 0.00 0.00 0.00 3.24
1643 1663 8.713271 GGAAAGTTCTAGTTGTAATGAAGAGTG 58.287 37.037 0.00 0.00 0.00 3.51
1644 1664 9.477484 GAAAGTTCTAGTTGTAATGAAGAGTGA 57.523 33.333 0.00 0.00 0.00 3.41
1645 1665 9.832445 AAAGTTCTAGTTGTAATGAAGAGTGAA 57.168 29.630 0.00 0.00 0.00 3.18
1646 1666 9.482627 AAGTTCTAGTTGTAATGAAGAGTGAAG 57.517 33.333 0.00 0.00 0.00 3.02
1647 1667 8.861086 AGTTCTAGTTGTAATGAAGAGTGAAGA 58.139 33.333 0.00 0.00 0.00 2.87
1648 1668 9.134734 GTTCTAGTTGTAATGAAGAGTGAAGAG 57.865 37.037 0.00 0.00 0.00 2.85
1649 1669 8.637196 TCTAGTTGTAATGAAGAGTGAAGAGA 57.363 34.615 0.00 0.00 0.00 3.10
1650 1670 9.078990 TCTAGTTGTAATGAAGAGTGAAGAGAA 57.921 33.333 0.00 0.00 0.00 2.87
1651 1671 9.698309 CTAGTTGTAATGAAGAGTGAAGAGAAA 57.302 33.333 0.00 0.00 0.00 2.52
1652 1672 8.964476 AGTTGTAATGAAGAGTGAAGAGAAAA 57.036 30.769 0.00 0.00 0.00 2.29
1653 1673 9.396022 AGTTGTAATGAAGAGTGAAGAGAAAAA 57.604 29.630 0.00 0.00 0.00 1.94
1660 1680 7.861630 TGAAGAGTGAAGAGAAAAATAAACCG 58.138 34.615 0.00 0.00 0.00 4.44
1661 1681 7.713507 TGAAGAGTGAAGAGAAAAATAAACCGA 59.286 33.333 0.00 0.00 0.00 4.69
1662 1682 8.622948 AAGAGTGAAGAGAAAAATAAACCGAT 57.377 30.769 0.00 0.00 0.00 4.18
1663 1683 8.034058 AGAGTGAAGAGAAAAATAAACCGATG 57.966 34.615 0.00 0.00 0.00 3.84
1664 1684 7.878127 AGAGTGAAGAGAAAAATAAACCGATGA 59.122 33.333 0.00 0.00 0.00 2.92
1665 1685 8.391075 AGTGAAGAGAAAAATAAACCGATGAA 57.609 30.769 0.00 0.00 0.00 2.57
1666 1686 8.290325 AGTGAAGAGAAAAATAAACCGATGAAC 58.710 33.333 0.00 0.00 0.00 3.18
1667 1687 7.537649 GTGAAGAGAAAAATAAACCGATGAACC 59.462 37.037 0.00 0.00 0.00 3.62
1668 1688 7.229707 TGAAGAGAAAAATAAACCGATGAACCA 59.770 33.333 0.00 0.00 0.00 3.67
1669 1689 7.145932 AGAGAAAAATAAACCGATGAACCAG 57.854 36.000 0.00 0.00 0.00 4.00
1670 1690 6.151144 AGAGAAAAATAAACCGATGAACCAGG 59.849 38.462 0.00 0.00 0.00 4.45
1671 1691 5.185056 AGAAAAATAAACCGATGAACCAGGG 59.815 40.000 0.00 0.00 0.00 4.45
1672 1692 3.732048 AATAAACCGATGAACCAGGGT 57.268 42.857 0.00 0.00 0.00 4.34
1673 1693 2.483014 TAAACCGATGAACCAGGGTG 57.517 50.000 0.00 0.00 31.96 4.61
1674 1694 0.251165 AAACCGATGAACCAGGGTGG 60.251 55.000 0.00 0.00 45.02 4.61
1675 1695 2.137177 AACCGATGAACCAGGGTGGG 62.137 60.000 0.00 0.00 43.37 4.61
1676 1696 2.297895 CCGATGAACCAGGGTGGGA 61.298 63.158 0.00 0.00 43.37 4.37
1677 1697 1.221840 CGATGAACCAGGGTGGGAG 59.778 63.158 0.00 0.00 43.37 4.30
1678 1698 1.609783 GATGAACCAGGGTGGGAGG 59.390 63.158 0.00 0.00 43.37 4.30
1679 1699 1.926426 GATGAACCAGGGTGGGAGGG 61.926 65.000 0.00 0.00 43.37 4.30
1680 1700 3.339093 GAACCAGGGTGGGAGGGG 61.339 72.222 0.00 0.00 43.37 4.79
1692 1712 4.348495 GAGGGGGTGGTGGGAGGA 62.348 72.222 0.00 0.00 0.00 3.71
1693 1713 4.354943 AGGGGGTGGTGGGAGGAG 62.355 72.222 0.00 0.00 0.00 3.69
1694 1714 4.348495 GGGGGTGGTGGGAGGAGA 62.348 72.222 0.00 0.00 0.00 3.71
1695 1715 2.689034 GGGGTGGTGGGAGGAGAG 60.689 72.222 0.00 0.00 0.00 3.20
1696 1716 2.450243 GGGTGGTGGGAGGAGAGA 59.550 66.667 0.00 0.00 0.00 3.10
1697 1717 1.990614 GGGTGGTGGGAGGAGAGAC 60.991 68.421 0.00 0.00 0.00 3.36
1698 1718 2.352032 GGTGGTGGGAGGAGAGACG 61.352 68.421 0.00 0.00 0.00 4.18
1699 1719 1.304217 GTGGTGGGAGGAGAGACGA 60.304 63.158 0.00 0.00 0.00 4.20
1700 1720 0.898789 GTGGTGGGAGGAGAGACGAA 60.899 60.000 0.00 0.00 0.00 3.85
1701 1721 0.178944 TGGTGGGAGGAGAGACGAAA 60.179 55.000 0.00 0.00 0.00 3.46
1702 1722 0.974383 GGTGGGAGGAGAGACGAAAA 59.026 55.000 0.00 0.00 0.00 2.29
1703 1723 1.346722 GGTGGGAGGAGAGACGAAAAA 59.653 52.381 0.00 0.00 0.00 1.94
1722 1742 3.994204 AAACCAGCGAAAATAAACCGT 57.006 38.095 0.00 0.00 0.00 4.83
1723 1743 2.981400 ACCAGCGAAAATAAACCGTG 57.019 45.000 0.00 0.00 0.00 4.94
1724 1744 1.538075 ACCAGCGAAAATAAACCGTGG 59.462 47.619 0.00 0.00 33.76 4.94
1725 1745 1.807742 CCAGCGAAAATAAACCGTGGA 59.192 47.619 0.00 0.00 31.24 4.02
1726 1746 2.159572 CCAGCGAAAATAAACCGTGGAG 60.160 50.000 0.00 0.00 31.24 3.86
1727 1747 2.739913 CAGCGAAAATAAACCGTGGAGA 59.260 45.455 0.00 0.00 0.00 3.71
1728 1748 2.740447 AGCGAAAATAAACCGTGGAGAC 59.260 45.455 0.00 0.00 0.00 3.36
1729 1749 2.740447 GCGAAAATAAACCGTGGAGACT 59.260 45.455 0.00 0.00 0.00 3.24
1730 1750 3.928375 GCGAAAATAAACCGTGGAGACTA 59.072 43.478 0.00 0.00 0.00 2.59
1731 1751 4.569564 GCGAAAATAAACCGTGGAGACTAT 59.430 41.667 0.00 0.00 0.00 2.12
1732 1752 5.064325 GCGAAAATAAACCGTGGAGACTATT 59.936 40.000 0.00 0.00 0.00 1.73
1733 1753 6.702897 CGAAAATAAACCGTGGAGACTATTC 58.297 40.000 0.00 0.00 0.00 1.75
1734 1754 6.311935 CGAAAATAAACCGTGGAGACTATTCA 59.688 38.462 0.00 0.00 0.00 2.57
1735 1755 6.980051 AAATAAACCGTGGAGACTATTCAC 57.020 37.500 0.00 0.00 0.00 3.18
1736 1756 3.329929 AAACCGTGGAGACTATTCACC 57.670 47.619 0.00 0.00 33.22 4.02
1737 1757 1.933021 ACCGTGGAGACTATTCACCA 58.067 50.000 0.00 0.00 39.94 4.17
1738 1758 2.253610 ACCGTGGAGACTATTCACCAA 58.746 47.619 0.79 0.00 43.35 3.67
1739 1759 2.028385 ACCGTGGAGACTATTCACCAAC 60.028 50.000 0.79 0.00 43.35 3.77
1740 1760 2.233922 CCGTGGAGACTATTCACCAACT 59.766 50.000 0.79 0.00 43.35 3.16
1741 1761 3.512680 CGTGGAGACTATTCACCAACTC 58.487 50.000 0.79 0.00 43.35 3.01
1742 1762 3.512680 GTGGAGACTATTCACCAACTCG 58.487 50.000 0.79 0.00 43.35 4.18
1743 1763 3.056749 GTGGAGACTATTCACCAACTCGT 60.057 47.826 0.79 0.00 43.35 4.18
1744 1764 3.192844 TGGAGACTATTCACCAACTCGTC 59.807 47.826 0.00 0.00 39.34 4.20
1745 1765 3.429135 GGAGACTATTCACCAACTCGTCC 60.429 52.174 0.00 0.00 32.87 4.79
1746 1766 3.162666 AGACTATTCACCAACTCGTCCA 58.837 45.455 0.00 0.00 0.00 4.02
1747 1767 3.769844 AGACTATTCACCAACTCGTCCAT 59.230 43.478 0.00 0.00 0.00 3.41
1748 1768 4.223032 AGACTATTCACCAACTCGTCCATT 59.777 41.667 0.00 0.00 0.00 3.16
1749 1769 5.421056 AGACTATTCACCAACTCGTCCATTA 59.579 40.000 0.00 0.00 0.00 1.90
1750 1770 5.661458 ACTATTCACCAACTCGTCCATTAG 58.339 41.667 0.00 0.00 0.00 1.73
1751 1771 3.328382 TTCACCAACTCGTCCATTAGG 57.672 47.619 0.00 0.00 0.00 2.69
1752 1772 2.531771 TCACCAACTCGTCCATTAGGA 58.468 47.619 0.00 0.00 43.21 2.94
1764 1784 5.067273 CGTCCATTAGGAGTAGAGATGACT 58.933 45.833 0.00 0.00 46.92 3.41
1864 1884 3.322211 TCGGTCGAACCACATAACAAT 57.678 42.857 0.00 0.00 38.47 2.71
1887 1908 2.925724 ACGTTGTTCCCTTTGTCATCA 58.074 42.857 0.00 0.00 0.00 3.07
1917 1938 1.101635 TGCCCGAGATTCGATCGTCT 61.102 55.000 15.94 11.59 43.74 4.18
1923 1945 3.536833 CGAGATTCGATCGTCTGTACTG 58.463 50.000 15.94 0.00 43.74 2.74
1987 2009 4.604976 GTTCTGTAATGCATCATTCTGCC 58.395 43.478 0.00 0.00 41.58 4.85
2000 2022 6.206243 GCATCATTCTGCCACTAACTCATTAT 59.794 38.462 0.00 0.00 36.10 1.28
2116 2139 1.588674 TGCCAACTCAACAAGTACCG 58.411 50.000 0.00 0.00 37.17 4.02
2179 2202 2.025589 TGTGACGTTTGGTAGCACAA 57.974 45.000 0.00 0.00 36.63 3.33
2181 2204 2.946329 TGTGACGTTTGGTAGCACAAAT 59.054 40.909 0.00 0.00 41.80 2.32
2295 2320 3.585862 TCAAGTGCTAAGCTAACGGAAG 58.414 45.455 0.00 0.00 0.00 3.46
2297 2322 2.176889 AGTGCTAAGCTAACGGAAGGA 58.823 47.619 0.00 0.00 0.00 3.36
2299 2324 1.134788 TGCTAAGCTAACGGAAGGAGC 60.135 52.381 0.00 0.00 42.48 4.70
2393 2419 9.093458 AGGAAACTTAACCATCTTTGATTCAAT 57.907 29.630 0.00 0.00 37.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.908483 GGCTCGGGAACAGGAGAAT 59.092 57.895 0.00 0.00 33.17 2.40
81 83 1.925285 ATTCCCCTTCGATGCCAGCA 61.925 55.000 0.00 0.00 0.00 4.41
200 204 2.172293 GGCATCTGACTTCCTCCAGATT 59.828 50.000 0.00 0.00 45.01 2.40
208 212 2.109126 GCCGTGGCATCTGACTTCC 61.109 63.158 5.89 0.00 41.49 3.46
269 273 0.615331 CCTTGACAAGCTCCTAGCCA 59.385 55.000 9.85 0.00 43.77 4.75
285 289 2.508586 GAAGGCGTTCGGAGCTCCTT 62.509 60.000 29.73 14.81 39.63 3.36
313 317 0.108186 TTGATCTCGTTGGCGCAGAT 60.108 50.000 10.83 8.50 37.54 2.90
361 365 0.396811 CCCAAGGTTGAGGAAGACGT 59.603 55.000 0.00 0.00 0.00 4.34
388 392 0.719465 GCGGATCGAACGACAATGTT 59.281 50.000 15.77 0.00 34.02 2.71
420 424 1.307647 CCTTGGGGAAGACATGGGG 59.692 63.158 0.00 0.00 33.58 4.96
435 439 2.676471 GGTGTCAATGGCGCCCTT 60.676 61.111 26.77 18.94 0.00 3.95
513 523 3.700970 TGATTCTCGGCCACGGCA 61.701 61.111 10.83 0.00 44.11 5.69
533 543 3.228759 GCAATGGCCATGGCGGAT 61.229 61.111 29.14 20.87 43.06 4.18
552 562 3.075005 GAGCTCGGTGGCTACCCA 61.075 66.667 14.41 0.00 44.53 4.51
594 604 2.501128 GGCGTGCATAGGAGCTGA 59.499 61.111 0.00 0.00 34.99 4.26
747 758 2.904866 GCCAGGGTTTGTGTCGCA 60.905 61.111 0.00 0.00 0.00 5.10
809 824 1.122019 GGGTGAGCGATGGGATAGGT 61.122 60.000 0.00 0.00 0.00 3.08
881 896 1.999634 GACATGGATGAGGGGGTGGG 62.000 65.000 0.00 0.00 0.00 4.61
897 912 4.819761 GCAGAGATGCGGCCGACA 62.820 66.667 33.48 26.38 0.00 4.35
951 966 2.169663 CGCATAGCAACAAGAAGCAG 57.830 50.000 0.00 0.00 0.00 4.24
1100 1115 2.510411 CACAGCCAGGTGACACCA 59.490 61.111 26.30 0.00 41.95 4.17
1312 1331 8.579006 TGCATAGAAATCAGTTCAAAAATCACT 58.421 29.630 0.00 0.00 38.86 3.41
1313 1332 8.746922 TGCATAGAAATCAGTTCAAAAATCAC 57.253 30.769 0.00 0.00 38.86 3.06
1314 1333 9.761504 TTTGCATAGAAATCAGTTCAAAAATCA 57.238 25.926 0.00 0.00 38.86 2.57
1349 1369 4.557205 ACTTTCCTAATCAGACACGTCAC 58.443 43.478 0.00 0.00 0.00 3.67
1350 1370 4.866508 ACTTTCCTAATCAGACACGTCA 57.133 40.909 0.00 0.00 0.00 4.35
1351 1371 5.614887 GCAAACTTTCCTAATCAGACACGTC 60.615 44.000 0.00 0.00 0.00 4.34
1352 1372 4.213482 GCAAACTTTCCTAATCAGACACGT 59.787 41.667 0.00 0.00 0.00 4.49
1353 1373 4.213270 TGCAAACTTTCCTAATCAGACACG 59.787 41.667 0.00 0.00 0.00 4.49
1354 1374 5.689383 TGCAAACTTTCCTAATCAGACAC 57.311 39.130 0.00 0.00 0.00 3.67
1355 1375 6.707440 TTTGCAAACTTTCCTAATCAGACA 57.293 33.333 8.05 0.00 0.00 3.41
1356 1376 7.147976 ACATTTGCAAACTTTCCTAATCAGAC 58.852 34.615 15.41 0.00 0.00 3.51
1357 1377 7.288810 ACATTTGCAAACTTTCCTAATCAGA 57.711 32.000 15.41 0.00 0.00 3.27
1358 1378 7.951530 AACATTTGCAAACTTTCCTAATCAG 57.048 32.000 15.41 0.00 0.00 2.90
1359 1379 9.474920 CTTAACATTTGCAAACTTTCCTAATCA 57.525 29.630 15.41 0.00 0.00 2.57
1360 1380 9.691362 TCTTAACATTTGCAAACTTTCCTAATC 57.309 29.630 15.41 0.00 0.00 1.75
1362 1382 9.877178 TTTCTTAACATTTGCAAACTTTCCTAA 57.123 25.926 15.41 6.03 0.00 2.69
1363 1383 9.308318 GTTTCTTAACATTTGCAAACTTTCCTA 57.692 29.630 15.41 0.00 34.31 2.94
1364 1384 8.040727 AGTTTCTTAACATTTGCAAACTTTCCT 58.959 29.630 15.41 0.00 36.70 3.36
1365 1385 8.196802 AGTTTCTTAACATTTGCAAACTTTCC 57.803 30.769 15.41 0.00 36.70 3.13
1383 1403 9.601810 AACTTTCCTCCCAATAAATAGTTTCTT 57.398 29.630 0.00 0.00 0.00 2.52
1384 1404 9.025041 CAACTTTCCTCCCAATAAATAGTTTCT 57.975 33.333 0.00 0.00 0.00 2.52
1385 1405 8.803235 ACAACTTTCCTCCCAATAAATAGTTTC 58.197 33.333 0.00 0.00 0.00 2.78
1386 1406 8.585018 CACAACTTTCCTCCCAATAAATAGTTT 58.415 33.333 0.00 0.00 0.00 2.66
1387 1407 7.947890 TCACAACTTTCCTCCCAATAAATAGTT 59.052 33.333 0.00 0.00 0.00 2.24
1388 1408 7.393515 GTCACAACTTTCCTCCCAATAAATAGT 59.606 37.037 0.00 0.00 0.00 2.12
1389 1409 7.414098 CGTCACAACTTTCCTCCCAATAAATAG 60.414 40.741 0.00 0.00 0.00 1.73
1390 1410 6.373216 CGTCACAACTTTCCTCCCAATAAATA 59.627 38.462 0.00 0.00 0.00 1.40
1391 1411 5.183140 CGTCACAACTTTCCTCCCAATAAAT 59.817 40.000 0.00 0.00 0.00 1.40
1392 1412 4.517453 CGTCACAACTTTCCTCCCAATAAA 59.483 41.667 0.00 0.00 0.00 1.40
1393 1413 4.069304 CGTCACAACTTTCCTCCCAATAA 58.931 43.478 0.00 0.00 0.00 1.40
1394 1414 3.071892 ACGTCACAACTTTCCTCCCAATA 59.928 43.478 0.00 0.00 0.00 1.90
1395 1415 2.158667 ACGTCACAACTTTCCTCCCAAT 60.159 45.455 0.00 0.00 0.00 3.16
1396 1416 1.210967 ACGTCACAACTTTCCTCCCAA 59.789 47.619 0.00 0.00 0.00 4.12
1397 1417 0.834612 ACGTCACAACTTTCCTCCCA 59.165 50.000 0.00 0.00 0.00 4.37
1398 1418 1.226746 CACGTCACAACTTTCCTCCC 58.773 55.000 0.00 0.00 0.00 4.30
1399 1419 1.865340 GACACGTCACAACTTTCCTCC 59.135 52.381 0.00 0.00 0.00 4.30
1400 1420 2.540101 CAGACACGTCACAACTTTCCTC 59.460 50.000 0.00 0.00 0.00 3.71
1401 1421 2.093658 ACAGACACGTCACAACTTTCCT 60.094 45.455 0.00 0.00 0.00 3.36
1402 1422 2.277084 ACAGACACGTCACAACTTTCC 58.723 47.619 0.00 0.00 0.00 3.13
1403 1423 5.652744 ATAACAGACACGTCACAACTTTC 57.347 39.130 0.00 0.00 0.00 2.62
1404 1424 6.128117 ACAAATAACAGACACGTCACAACTTT 60.128 34.615 0.00 0.00 0.00 2.66
1405 1425 5.353123 ACAAATAACAGACACGTCACAACTT 59.647 36.000 0.00 0.00 0.00 2.66
1406 1426 4.873827 ACAAATAACAGACACGTCACAACT 59.126 37.500 0.00 0.00 0.00 3.16
1407 1427 5.151632 ACAAATAACAGACACGTCACAAC 57.848 39.130 0.00 0.00 0.00 3.32
1408 1428 5.804692 AACAAATAACAGACACGTCACAA 57.195 34.783 0.00 0.00 0.00 3.33
1409 1429 5.220700 GGAAACAAATAACAGACACGTCACA 60.221 40.000 0.00 0.00 0.00 3.58
1410 1430 5.007332 AGGAAACAAATAACAGACACGTCAC 59.993 40.000 0.00 0.00 0.00 3.67
1411 1431 5.120399 AGGAAACAAATAACAGACACGTCA 58.880 37.500 0.00 0.00 0.00 4.35
1412 1432 5.668558 AGGAAACAAATAACAGACACGTC 57.331 39.130 0.00 0.00 0.00 4.34
1413 1433 7.556733 TTTAGGAAACAAATAACAGACACGT 57.443 32.000 0.00 0.00 0.00 4.49
1414 1434 8.265220 GTTTTAGGAAACAAATAACAGACACG 57.735 34.615 0.00 0.00 43.65 4.49
1506 1526 9.883142 ACAAATAACAGATTTTCAGGAAACAAA 57.117 25.926 0.00 0.00 0.00 2.83
1507 1527 9.883142 AACAAATAACAGATTTTCAGGAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
1508 1528 9.883142 AAACAAATAACAGATTTTCAGGAAACA 57.117 25.926 0.00 0.00 0.00 2.83
1510 1530 9.541143 GGAAACAAATAACAGATTTTCAGGAAA 57.459 29.630 0.00 0.00 0.00 3.13
1511 1531 8.923270 AGGAAACAAATAACAGATTTTCAGGAA 58.077 29.630 0.00 0.00 0.00 3.36
1512 1532 8.477419 AGGAAACAAATAACAGATTTTCAGGA 57.523 30.769 0.00 0.00 0.00 3.86
1528 1548 7.841956 TGGTTCAATTTGTCTTAGGAAACAAA 58.158 30.769 3.45 3.45 46.16 2.83
1529 1549 7.411486 TGGTTCAATTTGTCTTAGGAAACAA 57.589 32.000 0.00 0.00 29.84 2.83
1530 1550 7.411486 TTGGTTCAATTTGTCTTAGGAAACA 57.589 32.000 0.00 0.00 30.79 2.83
1531 1551 9.974980 TTATTGGTTCAATTTGTCTTAGGAAAC 57.025 29.630 0.00 0.00 35.54 2.78
1535 1555 9.423061 CCTTTTATTGGTTCAATTTGTCTTAGG 57.577 33.333 0.00 0.00 35.54 2.69
1539 1559 9.710900 GATTCCTTTTATTGGTTCAATTTGTCT 57.289 29.630 0.00 0.00 35.54 3.41
1540 1560 8.647226 CGATTCCTTTTATTGGTTCAATTTGTC 58.353 33.333 0.00 0.00 35.54 3.18
1541 1561 8.364142 TCGATTCCTTTTATTGGTTCAATTTGT 58.636 29.630 0.00 0.00 35.54 2.83
1542 1562 8.755696 TCGATTCCTTTTATTGGTTCAATTTG 57.244 30.769 0.00 0.00 35.54 2.32
1543 1563 9.942850 AATCGATTCCTTTTATTGGTTCAATTT 57.057 25.926 4.39 0.00 35.54 1.82
1544 1564 9.369904 CAATCGATTCCTTTTATTGGTTCAATT 57.630 29.630 7.92 0.00 35.54 2.32
1545 1565 8.748412 TCAATCGATTCCTTTTATTGGTTCAAT 58.252 29.630 7.92 0.00 37.80 2.57
1546 1566 8.116651 TCAATCGATTCCTTTTATTGGTTCAA 57.883 30.769 7.92 0.00 0.00 2.69
1547 1567 7.695480 TCAATCGATTCCTTTTATTGGTTCA 57.305 32.000 7.92 0.00 0.00 3.18
1548 1568 9.586435 AAATCAATCGATTCCTTTTATTGGTTC 57.414 29.630 7.92 0.00 41.12 3.62
1549 1569 9.369904 CAAATCAATCGATTCCTTTTATTGGTT 57.630 29.630 7.92 0.00 41.12 3.67
1550 1570 7.492344 GCAAATCAATCGATTCCTTTTATTGGT 59.508 33.333 7.92 0.00 41.12 3.67
1551 1571 7.492020 TGCAAATCAATCGATTCCTTTTATTGG 59.508 33.333 7.92 1.25 41.12 3.16
1552 1572 8.410030 TGCAAATCAATCGATTCCTTTTATTG 57.590 30.769 7.92 8.01 41.12 1.90
1556 1576 9.603921 AATTATGCAAATCAATCGATTCCTTTT 57.396 25.926 7.92 5.75 41.12 2.27
1557 1577 9.603921 AAATTATGCAAATCAATCGATTCCTTT 57.396 25.926 7.92 8.03 41.12 3.11
1564 1584 9.734620 CTTCCTTAAATTATGCAAATCAATCGA 57.265 29.630 0.00 0.00 0.00 3.59
1565 1585 9.520204 ACTTCCTTAAATTATGCAAATCAATCG 57.480 29.630 0.00 0.00 0.00 3.34
1573 1593 9.920946 AGGATCTAACTTCCTTAAATTATGCAA 57.079 29.630 0.00 0.00 40.84 4.08
1593 1613 9.225682 TCCTAACCTATAACAAATCAAGGATCT 57.774 33.333 0.00 0.00 0.00 2.75
1594 1614 9.847224 TTCCTAACCTATAACAAATCAAGGATC 57.153 33.333 0.00 0.00 29.99 3.36
1596 1616 9.681062 CTTTCCTAACCTATAACAAATCAAGGA 57.319 33.333 0.00 0.00 0.00 3.36
1597 1617 9.462606 ACTTTCCTAACCTATAACAAATCAAGG 57.537 33.333 0.00 0.00 0.00 3.61
1611 1631 8.877195 TCATTACAACTAGAACTTTCCTAACCT 58.123 33.333 0.00 0.00 0.00 3.50
1612 1632 9.498176 TTCATTACAACTAGAACTTTCCTAACC 57.502 33.333 0.00 0.00 0.00 2.85
1616 1636 8.652290 ACTCTTCATTACAACTAGAACTTTCCT 58.348 33.333 0.00 0.00 0.00 3.36
1617 1637 8.713271 CACTCTTCATTACAACTAGAACTTTCC 58.287 37.037 0.00 0.00 0.00 3.13
1618 1638 9.477484 TCACTCTTCATTACAACTAGAACTTTC 57.523 33.333 0.00 0.00 0.00 2.62
1619 1639 9.832445 TTCACTCTTCATTACAACTAGAACTTT 57.168 29.630 0.00 0.00 0.00 2.66
1620 1640 9.482627 CTTCACTCTTCATTACAACTAGAACTT 57.517 33.333 0.00 0.00 0.00 2.66
1621 1641 8.861086 TCTTCACTCTTCATTACAACTAGAACT 58.139 33.333 0.00 0.00 0.00 3.01
1622 1642 9.134734 CTCTTCACTCTTCATTACAACTAGAAC 57.865 37.037 0.00 0.00 0.00 3.01
1623 1643 9.078990 TCTCTTCACTCTTCATTACAACTAGAA 57.921 33.333 0.00 0.00 0.00 2.10
1624 1644 8.637196 TCTCTTCACTCTTCATTACAACTAGA 57.363 34.615 0.00 0.00 0.00 2.43
1625 1645 9.698309 TTTCTCTTCACTCTTCATTACAACTAG 57.302 33.333 0.00 0.00 0.00 2.57
1627 1647 8.964476 TTTTCTCTTCACTCTTCATTACAACT 57.036 30.769 0.00 0.00 0.00 3.16
1634 1654 8.507249 CGGTTTATTTTTCTCTTCACTCTTCAT 58.493 33.333 0.00 0.00 0.00 2.57
1635 1655 7.713507 TCGGTTTATTTTTCTCTTCACTCTTCA 59.286 33.333 0.00 0.00 0.00 3.02
1636 1656 8.084590 TCGGTTTATTTTTCTCTTCACTCTTC 57.915 34.615 0.00 0.00 0.00 2.87
1637 1657 8.507249 CATCGGTTTATTTTTCTCTTCACTCTT 58.493 33.333 0.00 0.00 0.00 2.85
1638 1658 7.878127 TCATCGGTTTATTTTTCTCTTCACTCT 59.122 33.333 0.00 0.00 0.00 3.24
1639 1659 8.029642 TCATCGGTTTATTTTTCTCTTCACTC 57.970 34.615 0.00 0.00 0.00 3.51
1640 1660 7.979444 TCATCGGTTTATTTTTCTCTTCACT 57.021 32.000 0.00 0.00 0.00 3.41
1641 1661 7.537649 GGTTCATCGGTTTATTTTTCTCTTCAC 59.462 37.037 0.00 0.00 0.00 3.18
1642 1662 7.229707 TGGTTCATCGGTTTATTTTTCTCTTCA 59.770 33.333 0.00 0.00 0.00 3.02
1643 1663 7.590279 TGGTTCATCGGTTTATTTTTCTCTTC 58.410 34.615 0.00 0.00 0.00 2.87
1644 1664 7.309194 CCTGGTTCATCGGTTTATTTTTCTCTT 60.309 37.037 0.00 0.00 0.00 2.85
1645 1665 6.151144 CCTGGTTCATCGGTTTATTTTTCTCT 59.849 38.462 0.00 0.00 0.00 3.10
1646 1666 6.322491 CCTGGTTCATCGGTTTATTTTTCTC 58.678 40.000 0.00 0.00 0.00 2.87
1647 1667 5.185056 CCCTGGTTCATCGGTTTATTTTTCT 59.815 40.000 0.00 0.00 0.00 2.52
1648 1668 5.047590 ACCCTGGTTCATCGGTTTATTTTTC 60.048 40.000 0.00 0.00 0.00 2.29
1649 1669 4.836175 ACCCTGGTTCATCGGTTTATTTTT 59.164 37.500 0.00 0.00 0.00 1.94
1650 1670 4.219725 CACCCTGGTTCATCGGTTTATTTT 59.780 41.667 0.00 0.00 0.00 1.82
1651 1671 3.761752 CACCCTGGTTCATCGGTTTATTT 59.238 43.478 0.00 0.00 0.00 1.40
1652 1672 3.352648 CACCCTGGTTCATCGGTTTATT 58.647 45.455 0.00 0.00 0.00 1.40
1653 1673 2.356741 CCACCCTGGTTCATCGGTTTAT 60.357 50.000 0.00 0.00 31.35 1.40
1654 1674 1.003812 CCACCCTGGTTCATCGGTTTA 59.996 52.381 0.00 0.00 31.35 2.01
1655 1675 0.251165 CCACCCTGGTTCATCGGTTT 60.251 55.000 0.00 0.00 31.35 3.27
1656 1676 1.378762 CCACCCTGGTTCATCGGTT 59.621 57.895 0.00 0.00 31.35 4.44
1657 1677 2.602676 CCCACCCTGGTTCATCGGT 61.603 63.158 0.00 0.00 35.17 4.69
1658 1678 2.257409 CTCCCACCCTGGTTCATCGG 62.257 65.000 0.00 0.00 35.17 4.18
1659 1679 1.221840 CTCCCACCCTGGTTCATCG 59.778 63.158 0.00 0.00 35.17 3.84
1660 1680 1.609783 CCTCCCACCCTGGTTCATC 59.390 63.158 0.00 0.00 35.17 2.92
1661 1681 1.930656 CCCTCCCACCCTGGTTCAT 60.931 63.158 0.00 0.00 35.17 2.57
1662 1682 2.531685 CCCTCCCACCCTGGTTCA 60.532 66.667 0.00 0.00 35.17 3.18
1663 1683 3.339093 CCCCTCCCACCCTGGTTC 61.339 72.222 0.00 0.00 35.17 3.62
1675 1695 4.348495 TCCTCCCACCACCCCCTC 62.348 72.222 0.00 0.00 0.00 4.30
1676 1696 4.354943 CTCCTCCCACCACCCCCT 62.355 72.222 0.00 0.00 0.00 4.79
1677 1697 4.348495 TCTCCTCCCACCACCCCC 62.348 72.222 0.00 0.00 0.00 5.40
1678 1698 2.689034 CTCTCCTCCCACCACCCC 60.689 72.222 0.00 0.00 0.00 4.95
1679 1699 1.990614 GTCTCTCCTCCCACCACCC 60.991 68.421 0.00 0.00 0.00 4.61
1680 1700 2.352032 CGTCTCTCCTCCCACCACC 61.352 68.421 0.00 0.00 0.00 4.61
1681 1701 0.898789 TTCGTCTCTCCTCCCACCAC 60.899 60.000 0.00 0.00 0.00 4.16
1682 1702 0.178944 TTTCGTCTCTCCTCCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
1683 1703 0.974383 TTTTCGTCTCTCCTCCCACC 59.026 55.000 0.00 0.00 0.00 4.61
1684 1704 2.833631 TTTTTCGTCTCTCCTCCCAC 57.166 50.000 0.00 0.00 0.00 4.61
1700 1720 4.504826 CACGGTTTATTTTCGCTGGTTTTT 59.495 37.500 0.00 0.00 0.00 1.94
1701 1721 4.045783 CACGGTTTATTTTCGCTGGTTTT 58.954 39.130 0.00 0.00 0.00 2.43
1702 1722 3.551250 CCACGGTTTATTTTCGCTGGTTT 60.551 43.478 0.00 0.00 0.00 3.27
1703 1723 2.030628 CCACGGTTTATTTTCGCTGGTT 60.031 45.455 0.00 0.00 0.00 3.67
1704 1724 1.538075 CCACGGTTTATTTTCGCTGGT 59.462 47.619 0.00 0.00 0.00 4.00
1705 1725 1.807742 TCCACGGTTTATTTTCGCTGG 59.192 47.619 0.00 0.00 0.00 4.85
1706 1726 2.739913 TCTCCACGGTTTATTTTCGCTG 59.260 45.455 0.00 0.00 0.00 5.18
1707 1727 2.740447 GTCTCCACGGTTTATTTTCGCT 59.260 45.455 0.00 0.00 0.00 4.93
1708 1728 2.740447 AGTCTCCACGGTTTATTTTCGC 59.260 45.455 0.00 0.00 0.00 4.70
1709 1729 6.311935 TGAATAGTCTCCACGGTTTATTTTCG 59.688 38.462 0.00 0.00 0.00 3.46
1710 1730 7.413767 GGTGAATAGTCTCCACGGTTTATTTTC 60.414 40.741 6.41 0.00 37.37 2.29
1711 1731 6.373495 GGTGAATAGTCTCCACGGTTTATTTT 59.627 38.462 6.41 0.00 37.37 1.82
1712 1732 5.878669 GGTGAATAGTCTCCACGGTTTATTT 59.121 40.000 6.41 0.00 37.37 1.40
1713 1733 5.046159 TGGTGAATAGTCTCCACGGTTTATT 60.046 40.000 9.77 0.00 41.46 1.40
1714 1734 4.468510 TGGTGAATAGTCTCCACGGTTTAT 59.531 41.667 9.77 0.00 41.46 1.40
1715 1735 3.833650 TGGTGAATAGTCTCCACGGTTTA 59.166 43.478 9.77 0.00 41.46 2.01
1716 1736 2.635915 TGGTGAATAGTCTCCACGGTTT 59.364 45.455 9.77 0.00 41.46 3.27
1717 1737 2.253610 TGGTGAATAGTCTCCACGGTT 58.746 47.619 9.77 0.00 41.46 4.44
1718 1738 1.933021 TGGTGAATAGTCTCCACGGT 58.067 50.000 9.77 0.00 41.46 4.83
1719 1739 2.233922 AGTTGGTGAATAGTCTCCACGG 59.766 50.000 13.16 0.00 45.03 4.94
1720 1740 3.512680 GAGTTGGTGAATAGTCTCCACG 58.487 50.000 13.16 0.00 45.03 4.94
1721 1741 3.056749 ACGAGTTGGTGAATAGTCTCCAC 60.057 47.826 13.16 8.98 45.03 4.02
1722 1742 3.162666 ACGAGTTGGTGAATAGTCTCCA 58.837 45.455 9.77 9.77 43.97 3.86
1723 1743 3.429135 GGACGAGTTGGTGAATAGTCTCC 60.429 52.174 4.36 4.36 37.83 3.71
1724 1744 3.192844 TGGACGAGTTGGTGAATAGTCTC 59.807 47.826 0.00 0.00 0.00 3.36
1725 1745 3.162666 TGGACGAGTTGGTGAATAGTCT 58.837 45.455 0.00 0.00 0.00 3.24
1726 1746 3.587797 TGGACGAGTTGGTGAATAGTC 57.412 47.619 0.00 0.00 0.00 2.59
1727 1747 4.553330 AATGGACGAGTTGGTGAATAGT 57.447 40.909 0.00 0.00 0.00 2.12
1728 1748 5.050490 CCTAATGGACGAGTTGGTGAATAG 58.950 45.833 0.00 0.00 34.57 1.73
1729 1749 4.712829 TCCTAATGGACGAGTTGGTGAATA 59.287 41.667 0.00 0.00 37.46 1.75
1730 1750 3.517901 TCCTAATGGACGAGTTGGTGAAT 59.482 43.478 0.00 0.00 37.46 2.57
1731 1751 2.901192 TCCTAATGGACGAGTTGGTGAA 59.099 45.455 0.00 0.00 37.46 3.18
1732 1752 2.496070 CTCCTAATGGACGAGTTGGTGA 59.504 50.000 0.00 0.00 37.46 4.02
1733 1753 2.233922 ACTCCTAATGGACGAGTTGGTG 59.766 50.000 0.00 0.00 37.46 4.17
1734 1754 2.537143 ACTCCTAATGGACGAGTTGGT 58.463 47.619 0.00 0.00 37.46 3.67
1735 1755 3.952323 TCTACTCCTAATGGACGAGTTGG 59.048 47.826 0.00 0.00 37.93 3.77
1736 1756 4.882427 TCTCTACTCCTAATGGACGAGTTG 59.118 45.833 0.00 0.00 37.93 3.16
1737 1757 5.113446 TCTCTACTCCTAATGGACGAGTT 57.887 43.478 0.00 0.00 37.93 3.01
1738 1758 4.774660 TCTCTACTCCTAATGGACGAGT 57.225 45.455 0.00 0.00 40.00 4.18
1739 1759 5.180492 GTCATCTCTACTCCTAATGGACGAG 59.820 48.000 0.00 0.00 37.46 4.18
1740 1760 5.064558 GTCATCTCTACTCCTAATGGACGA 58.935 45.833 0.00 0.00 37.46 4.20
1741 1761 5.049060 CAGTCATCTCTACTCCTAATGGACG 60.049 48.000 0.00 0.00 37.46 4.79
1742 1762 6.065374 TCAGTCATCTCTACTCCTAATGGAC 58.935 44.000 0.00 0.00 37.46 4.02
1743 1763 6.101881 TCTCAGTCATCTCTACTCCTAATGGA 59.898 42.308 0.00 0.00 40.69 3.41
1744 1764 6.206634 GTCTCAGTCATCTCTACTCCTAATGG 59.793 46.154 0.00 0.00 0.00 3.16
1745 1765 6.770303 TGTCTCAGTCATCTCTACTCCTAATG 59.230 42.308 0.00 0.00 0.00 1.90
1746 1766 6.770785 GTGTCTCAGTCATCTCTACTCCTAAT 59.229 42.308 0.00 0.00 0.00 1.73
1747 1767 6.069905 AGTGTCTCAGTCATCTCTACTCCTAA 60.070 42.308 0.00 0.00 0.00 2.69
1748 1768 5.427157 AGTGTCTCAGTCATCTCTACTCCTA 59.573 44.000 0.00 0.00 0.00 2.94
1749 1769 4.227300 AGTGTCTCAGTCATCTCTACTCCT 59.773 45.833 0.00 0.00 0.00 3.69
1750 1770 4.523083 AGTGTCTCAGTCATCTCTACTCC 58.477 47.826 0.00 0.00 0.00 3.85
1751 1771 5.880332 AGAAGTGTCTCAGTCATCTCTACTC 59.120 44.000 0.00 0.00 0.00 2.59
1752 1772 5.815581 AGAAGTGTCTCAGTCATCTCTACT 58.184 41.667 0.00 0.00 0.00 2.57
1864 1884 5.795972 TGATGACAAAGGGAACAACGTATA 58.204 37.500 0.00 0.00 0.00 1.47
1887 1908 4.694339 GAATCTCGGGCAAGTAACATACT 58.306 43.478 0.00 0.00 41.73 2.12
1923 1945 9.420551 CCGGTAATAAGATTGAACTAGGTATTC 57.579 37.037 0.00 0.00 0.00 1.75
1987 2009 9.013490 GCAAGCAATGTAAATAATGAGTTAGTG 57.987 33.333 0.00 0.00 0.00 2.74
2000 2022 3.749665 AAGCCTTGCAAGCAATGTAAA 57.250 38.095 21.43 0.00 32.98 2.01
2116 2139 0.452585 GCTCTACAGGTGTCTCCGAC 59.547 60.000 0.00 0.00 41.99 4.79
2295 2320 2.715046 TGATGTGATTGACTTGGCTCC 58.285 47.619 0.00 0.00 0.00 4.70
2297 2322 4.597004 AGAATGATGTGATTGACTTGGCT 58.403 39.130 0.00 0.00 0.00 4.75
2299 2324 7.854557 TTAGAGAATGATGTGATTGACTTGG 57.145 36.000 0.00 0.00 0.00 3.61
2331 2357 5.180492 TGAGTTGTCATTTGATTAACGGGAC 59.820 40.000 0.00 0.00 32.73 4.46
2393 2419 3.087370 TGCCTCTACTTGACTAGCTCA 57.913 47.619 0.00 0.00 0.00 4.26


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.